2f7v: Difference between revisions

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[[Image:2f7v.gif|left|200px]]


{{Structure
==Structure of acetylcitrulline deacetylase complexed with one Co==
|PDB= 2f7v |SIZE=350|CAPTION= <scene name='initialview01'>2f7v</scene>, resolution 1.75&Aring;
<StructureSection load='2f7v' size='340' side='right'caption='[[2f7v]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CO:COBALT (II) ION'>CO</scene>
<table><tr><td colspan='2'>[[2f7v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris Xanthomonas campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F7V FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Acetylornithine_deacetylase Acetylornithine deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.16 3.5.1.16]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f7v OCA], [https://pdbe.org/2f7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f7v RCSB], [https://www.ebi.ac.uk/pdbsum/2f7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f7v ProSAT]</span></td></tr>
 
</table>
'''Structure of acetylcitrulline deacetylase complexed with one Co'''
== Function ==
 
[https://www.uniprot.org/uniprot/ACDAS_XANCP ACDAS_XANCP] Catalyzes the deacetylation of N-acetyl-L-citrulline to produce L-citrulline. This is a step in an alternative arginine biosynthesis pathway (PubMed:16585758, PubMed:16511126). Is also able to catalyze the deacetylation of N-acetylornithine in vitro, with almost equal velocity. However, this reaction may be not relevant in vivo since Xanthomonas does not possess the canonical argF gene and cannot convert ornithine to citrulline via ArgF' (PubMed:16585758).<ref>PMID:16511126</ref> <ref>PMID:16585758</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
The structure of a novel acetylcitrulline deacetylase from the plant pathogen Xanthomonas campestris has been solved by multiple-wavelength anomalous dispersion (MAD) using crystals grown from selenomethionine-substituted protein and refined at 1.75 A resolution. The asymmetric unit of the crystal contains one monomer consisting of two domains, a catalytic domain and a dimerization domain. The catalytic domain is able to bind a single Co(II) ion at the active site with no change in conformation. The dimerization domain forms an interface between two monomers related by a crystallographic two-fold symmetry axis. The interface is maintained by hydrophobic interactions between helices and hydrogen bonding between two beta strands that form a continuous beta sheet across the dimer interface. Because the dimers are also related by two-fold crystallographic axes, they pack together across the crystal via the dimerization domain, suggesting that higher order oligomers may form in solution. The polypeptide fold of the monomer is similar to the fold of Pseudomonas sp. carboxypeptidase G2 and Neisseria meningitidis succinyl diaminopimelate desuccinylase. Structural comparison among these enzymes allowed modeling of substrate binding and suggests a possible catalytic mechanism, in which Glu130 functions as a bifunctional general acid-base catalyst and the metal ion polarizes the carbonyl of the acetyl group.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/2f7v_consurf.spt"</scriptWhenChecked>
2F7V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Xanthomonas_campestris Xanthomonas campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F7V OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Structure of a novel N-acetyl-L-citrulline deacetylase from Xanthomonas campestris., Shi D, Yu X, Roth L, Tuchman M, Allewell NM, Biophys Chem. 2007 Mar;126(1-3):86-93. Epub 2006 Jun 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16750290 16750290]
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f7v ConSurf].
[[Category: Acetylornithine deacetylase]]
<div style="clear:both"></div>
[[Category: Single protein]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Xanthomonas campestris]]
[[Category: Xanthomonas campestris]]
[[Category: Allewell, N M.]]
[[Category: Allewell NM]]
[[Category: Roth, L.]]
[[Category: Roth L]]
[[Category: Shi, D.]]
[[Category: Shi D]]
[[Category: Tuchman, M.]]
[[Category: Tuchman M]]
[[Category: Yu, X.]]
[[Category: Yu X]]
[[Category: CO]]
[[Category: alpha/beta]]
 
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Retrieved from "https://proteopedia.org/2f7v"